Secondary structure and small RNA-seq evidence for dme-mir-2280

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2L:1831670-1831814 - TGGAGAAGAGTGATATCGTTTAAGATGC---------TGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACG--GACTAAAAATGCGTT-TG
droSim1 chr2L:1818710-1818856 - CGGAGCAGAGTGATATCGTTTGAGATGC---------TGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCG--GACTAAAAATGCTTTTTG
droSec1 super_14:1778365-1778510 - CGGAGCAAAGTGATATCGTTTGAAATGC---------TGTGAATATCCCGTTTTCTTTGCTTGGCAATAAAAT-ATTA------------------------------TTCACAGAAACTAGTAACTTACTT-----------CCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACG--GACTAAAAATGCTTTTTG
droYak2 chr2L:1804987-1805119 - CGGAGCAAACTGATGTCGTTTAGGATGC---------TGTGAATATCCCATTTTGTTAGCTTGGCAATAAAAT-ATTG------------------------------TTGATTGAAACTAGTAATTTACTT-----------CCAAGCTAACTGAAGTGGAT-ATTC--TA------------CAACAAATGGGTT-TT
droEre2 scaffold_4929:1878584-1878709 - CGGTG-----TGATTCTGCTTAAGGTGC---------TGTGAATATCCCATTTTCTTAGCTTGGCAATAAAAT-ATTA------------------------------TTCATCGA-ACTAGTAATTTAATT-----------CCAAGCCAACTAAAGGGGAT-ATTCACTG---------------CAAATGCATT-TG
droAna3 scaffold_12916:15757494-15757644 + CGTAGAAGCTT-AC-----TAGTTC--------------------------------TGTTTGGTAATAAAGT-TATTCTTTTTTATCTCAAAATGACTCACGTTTTTTTTTTCGA-ATCATTAAATAACATTTATATTTTCCCTAAGC-------CCTGAAT-ACTTATTATAAAAAAGACGATTATAAAAGTATA-TG
dp4 chr4_group3:8561836-8561913 - TGTTGTGGACTTAT-----CGGAGGAACTTGGCGAATTTTGATTATATTTTGATGCCATTTTT---------------------------------------------------------------------------------------ATCTGAAT-----------------------------AAAATGTTCT-TT
droPer1 super_1:10015828-10015916 - TGTTGTGGACTTAT-----CGGAGGAACTTGGCGAATTTTGATTATATTTAGATTCCATTTTT---------------------------------------------------------------------------------------ATCTGAATAAAAT-GTTC--TT---------------TAGTTACGTT-GA
droWil1 scaffold_180708:11841716-11841868 + TGCAGATGCCACAT-----CGGAATTGTGAAGGGAAAATGGGTTATTTAGTTGCGTTAGTTTAACGAGGAATGAAGGG------------------------------TCCGTTGTATTTAATTACTTTTTT----GGTAC--ATTAGTTAATAAAAGGAAAC-AATTAATCAATTAA----CATTATAAACTCGTT-TT
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2L:1831670-1831814 - TGGAGAAGAGTGATATCGTTTAAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACGGACTAAAAATGCGTT-TG
droSim1 chr2L:1818710-1818856 - CGGAGCAGAGTGATATCGTTTGAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCGGACTAAAAATGCTTTTTG
droSec1 super_14:1778365-1778510 - CGGAGCAAAGTGATATCGTTTGAAATGCTGTGAATATCCCGTTTTCTTTGCTTGGCAATAAAATATTATTCACAGAAACTAGTAACTTACTTCCAAGCTAACTGAAGGGGAT-ATTCAGTGCAACCACGGACTAAAAATGCTTTTTG
droYak2 chr2L:1804987-1805119 - CGGAGCAAACTGATGTCGTTTAGGATGCTGTGAATATCCCATTTTGTTAGCTTGGCAATAAAATATTGTTGATTGAAACTAGTAATTTACTTCCAAGCTAACTGAAGTGGAT-ATTC--TACAAC----------AAATGGGTT-TT
droEre2 scaffold_4929:1878584-1878709 - CGGT-----GTGATTCTGCTTAAGGTGCTGTGAATATCCCATTTTCTTAGCTTGGCAATAAAATATTATTCATCGA-ACTAGTAATTTAATTCCAAGCCAACTAAAGGGGAT-ATTCACTGCA-------------AATGCATT-TG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
CGGAGCAGAGTGATATCGT-------------------------TTGAGATGCTGTGAATATCCCGTTTTCTTAGCTTGGCAATAAAATATTATTCACAGAAACTAGTAATTTACTTCCAAGCTAACTGAAGGGGATTATTCAGTGCAACATCGGACTAAAAATGCTTTTTGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
TGTTGTGGACTTAT--CGGAGGAACTTGGCGAATTTTGATTATATTTTGATGCCATTT------------------------------------------------------------------------------------------TTATCTGAAT-AAAATGTTCT-TTSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-37.7 -37.5 -37.3 -37.2 -37.1 -37.0

droSim1

-35.8 -35.8 -35.4 -35.4 -35.3 -35.3

droSec1

-32.4 -32.2 -32.0 -31.9 -31.8 -31.8

droYak2

-30.9 -30.9 -30.9 -30.6 -30.6 -30.6

droEre2

-29.7 -29.5 -29.2 -29.2 -29.1 -29.1

droAna3

-10.89 -10.8 -10.8 -10.49 -10.4 -10.4

dp4

-9.5 -9.4 -9.2 -9.0 -8.9 -8.9

droPer1

-8.2 -8.0 -7.8 -7.4 -7.3 -7.2

droWil1

-15.2 -15.0 -14.9 -14.8 -14.8 -14.7

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:09 PM